[gmx-users] problem with g_cluster
sridhar at cdfd.org.in
sridhar at cdfd.org.in
Thu Jun 23 03:54:34 CEST 2005
Hi GMX users,
I have a problem with g_cluster. I am using g_cluster to cluster my
trajectory of 20000 structures
(20000ps). I am using the matrix file as input using option -dm. The
program gave error indicating memory fault initially. Later I ran the same
program using -skip 1000 option, thereby effectively reading only 20
structures, to check if it runs. Surprisingly the same problem repeats
even with this option. I am running on a intel(XEON dual
processor) machine with 2GB RAM and I think
it is sufficient for the process. I cannot figure out the problem.
Waiting for your suggessions.
I am attaching the output messages of the program below
#############################################################################
:-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens' Stories
:-) VERSION 3.2.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_cluster (-:
Option Filename Type Description
------------------------------------------------------------
-f traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96
pdb
-s /home/sridhar/CYP_NEWDYN/b4md_1cyp_WT.tpr Input, Opt!
Structure+mass(db): tpr tpb tpa gro g96
pdb xml
-n /home/sridhar/CYP_NEWDYN/b4ion_1cyp_WT.ndx Input, Opt! Index file
-dm ./RMSDMAT_WT.xpm Input, Opt! X PixMap compatible matrix file
-o rmsd-clust.xpm Output X PixMap compatible matrix file
-g cluster_WT.log Output Log file
-dist rmsd-dist.xvg Output, Opt. xvgr/xmgr file
-ev rmsd-eig.xvg Output, Opt. xvgr/xmgr file
-sz clust_size_WT.xvg Output, Opt! xvgr/xmgr file
-tr clust_trans_WT.xpm Output, Opt! X PixMap compatible matrix file
-ntr clust_Ntrans_WT.xvg Output, Opt! xvgr/xmgr file
-clid clust_it_WT.xvg Output, Opt! xvgr/xmgr file
-cl clusters_WT.pdb Output, Opt! Generic trajectory: xtc trr trj gro g96
pdb
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-b time -1 First frame (ps) to read from trajectory
-e time -1 Last frame (ps) to read from trajectory
-dt time -1 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]dista bool no Use RMSD of distances instead of RMS deviation
-nlevels int 40 Discretize RMSD matrix in # levels
-keepfree int -4 if >0 # levels not to use when coloring
clusters;
if <0 nlevels/-keepfree+1 levels will not be
used
-cutoff real 0.1 RMSD cut-off (nm) for two structures to be
neighbor
-[no]fit bool yes Use least squares fitting before RMSD
calculation
-max real -1 Maximum level in RMSD matrix
-skip int 1000 Only analyze every nr-th frame
-[no]av bool yes Write average iso middle structure for each
cluster
-wcl int 0 Write all structures for first # clusters to
numbered files
-nst int 1 Only write all structures if more than # per
cluster
-rmsmin real 0 minimum rms difference with rest of cluster
for
writing structures
-method enum jarvis-patrick Method for cluster determination:
linkage, jarvis-patrick, monte-carlo,
diagonalization or gromos
-minstruct int 1 Minimum number of structures in cluster for
coloring in the xpm file
-[no]binary bool no Treat the RMSD matrix as consisting of 0 and
1,
where the cut-off is given by -cutoff
-M int 10 Number of nearest neighbors considered for
Jarvis-Patrick algorithm, 0 is use cutoff
-P int 3 Number of identical nearest neighbors required
to
form a cluster
-seed int 1993 Random number seed for Monte Carlo clustering
algorithm
-niter int 10000 Number of iterations for MC
-kT real 0.001 Boltzmann weighting factor for Monte Carlo
optimization (zero turns off uphill steps)
Warning: cannot write cluster structures without reading trajectory
ignoring option -cl clusters_WT.pdb
Back Off! I just backed up cluster_WT.log to ./#cluster_WT.log.5#
Using jarvis-patrick method for clustering
Will use P=3, M=10 for determining the neighbors
Reading rms distance matrix 100%
Converted a 20001x20001 matrix with 80 levels to reals
The RMSD ranges from 0.0514 to 0.451 nm
Average RMSD is 0.0419409
Number of structures for matrix 20001
Energy of the matrix is 1854.48 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0514
Linking structures cluster.sh: line 2: 5007 Killed
g_cluster -dm ./RMSDMAT_$abc.xpm -s
/home/sridhar/CYP_NEWDYN/b4md_1cyp_$abc.tpr -n
/home/sridhar/CYP_NEWDYN/b4ion_1cyp_$abc.ndx -g cluster_$abc.log -sz
clust_size_$abc.xvg -tr clust_trans_$abc.xpm -ntr clust_Ntrans_$abc.xvg
-clid clust_it_$abc.xvg -cl clusters_$abc.pdb -av -method jarvis-patrick
-nice 0 -skip 1000
##########################################################################
thanks and waiting for your suggessions.
M. Sridhar Acharya
Senior Research Fellow
Lab. of Computational Biology
Centre for DNA Fingerprinting and Diagnostics
Hyderabad. 500076
Ph: +91-40-27151344-1207
Fax: +91-40-27155479
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